Fig. 2.

YDF allosterically inhibits the endopeptidase activity of HRV14 3C. (A) The protein–protein interface between HRV14 3C and YDF. HRV14 3C is shown as gray ribbons, with loop 107 to 114 and loop 138 to 145 highlighted in purple and pink, respectively. CDRH3 and the three light-chain CDRs of YDF that are involved in binding HRV14 3C are highlighted in cyan and blue, respectively. (B) Close-up views of the interface between CDRH3 (YDF) and HRV14 3C (Top) and the interface between CDRLs (YDF) and HRV14 3C (Bottom). Key residues that are involved in hydrophilic or hydrophobic interactions on protein–protein interfaces are shown as stick models and color-coded as in A. Polar and electrostatic interactions are indicated with black dashed lines. (Bottom) Electrostatic surface of HRV14 3C is shown to illustrate the hydrophobic cage that is formed by Y139, A140, K142, and F108 on HRV14 3C. Hydrophobic surfaces are in whitish gray, basic in blue, and acidic in red. The CDRs residues are labeled following Kabat numbering. (C) Protease activity (micromoles per second) of HRV14 3C was plotted against the concentration of substrate (micromolar) in the absence or presence of different molar ratios of YDF. The presence of YDF reduces V_max proportionally without affecting the apparent K_m of HRV14 3C, indicating that YDF is a noncompetitive inhibitor of HRV14 3C. Values are means ± SD (n = 3 assays).